calculateHeight: Calculate Peak Height.

Description

Calculate peak height metrics for samples.

Usage

calculateHeight(data, na = NULL, add = TRUE, exclude = NULL, sex.rm = FALSE, qs.rm = FALSE, kit = NULL, debug = FALSE)

Arguments

data

data.frame with at least columns 'Sample.Name' and 'Height'.

replaces NA values.

add

logical default is TRUE which will add/overwrite columns 'H', 'TPH', and 'Peaks' in the provided 'data'.

exclude

character vector (case sensitive) e.g. "OL" excludes rows with "OL" in the 'Allele' column.

sex.rm

logical, default FALSE to include sex markers in the analysis.

qs.rm

logical, default TRUE to exclude quality sensors from the analysis.

kit

character, required if sex.rm=TRUE or qs.rm=TRUE to define the kit.

debug

logical indicating printing debug information.

Value

data.frame with with at least columns 'Sample.Name', 'TPH', and 'Peaks'.

Details

Calculates the average peak height (H) and/or the total peak height (TPH) for each sample. To enable calculation of H the sample data must contain a column "Heterozygous", where 1 = heterozygous loci, and 0 = homozygous loci as known from the reference sample. Calculates H according to the formula: $H = sum(peak heights)/(n[het] + 2n[hom]$ Where: n[het] = number of observed heterozygous alleles n[hom] = number of observed homozygous alleles

References

Torben Tvedebrink, Poul Svante Eriksen, Helle Smidt Mogensen, Niels Morling, Evaluating the weight of evidence by using quantitative short tandem repeat data in DNA mixtures Journal of the Royal Statistical Society: Series C (Applied Statistics), Volume 59, Issue 5, 2010, Pages 855-874, 10.1111/j.1467-9876.2010.00722.x. http://dx.doi.org/10.1111/j.1467-9876.2010.00722.x